Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 103240 |
| Name | oriT_p4-IPM  |
| Organism | Klebsiella oxytoca strain pKOX3 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KY913900 (44237..44337 [+], 101 nt) |
| oriT length | 101 nt |
| IRs (inverted repeats) | 80..85, 91..96 (AAAAAA..TTTTTT) 20..26, 38..44 (TAAATCA..TGATTTA) |
| Location of nic site | 62..63 |
| Conserved sequence flanking the nic site |
GGTGTATAGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 101 nt
>oriT_p4-IPM
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG
TATTTATTTTTTTATCTTTTAAATCAGTATGATAGCGTGATTTATCGCGCTGCGTTAGGTGTATAGCAGGTTAAGGGATAAAAAATCATCTTTTTTGGTAG
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 2422 | GenBank | WP_227626566 |
| Name | TrwC_I3B51_RS00255_p4-IPM |
UniProt ID | _ |
| Length | 863 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 863 a.a. Molecular weight: 95911.42 Da Isoelectric Point: 9.6448
>WP_227626566.1 MobF family relaxase [Klebsiella oxytoca]
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQRA
MLDITTITRQNVTSVVGYYSDAKDDYYSKDSSFTSWQGTGAEALGLSGDVESARFKELLVGEIDTFTHMQ
RHVGDAKKERLGYDLTFSAPKGVSMQALIHGDKTIIEAHEKAVAAAVREAEKLAQARTTRQGKSVTQNTN
NLVVATFRHETSRALDPDLHTHAFVMNMTQREDGQWRALKNDELMRNKMHLGDVYKQELALELTKAGYEL
RYNSKNNTFDMAHFSDEQIRAFSRRSEQIEKGLAAMGLTRETADAQTKSRVSMATREKKTEHSREEIHQE
WASRAKTLGIDFDNREWQGHGKPLEADIARNMAPDFTSPEVKADRAIQFAVKSLSERDASFERQKLIQIA
NKQVLGHATMADVEKAYLKAVQKGAIIEGEARYQSTLKVGASVMAETLTRKEWIDSLTNSGMRADKARFA
VDDGIKNGRLKKTSHRVTTVEGIRLERSILTIESRGRGQMPRQLTAEIAGQLLAGKTLKNEQMRAVTEIV
TSKDRFVAAHGYAGTGKSYMTMAAKELLESQGLKVTALAPYGTQKKALEDDGLPARTVAAFLKAKDKKLD
EKSVVFIDEAGVIPARQMKQLMEVIEKHNARAVFLGDTSQTKAVEAGKPFEQLIKAGMQTSYMKDIQRQK
NEVLLEAVKYAAEGNAARALKNITGVNELKEEAPRLAQLADRYLSLSSEQQDATLIISGTNASRKTLNDY
IRGNLGLAGTGETFTLLDRVDSTQAERRDSRYFSKGQIIIPEQDYKNGMKRGESYQVLDTGPGNKLTVES
SSGEQIAFSPRTHTKLSVYQAVSAELAPGDKVMVTRNDKTLDVANGDRFTVKTVEGEKLTLEDKKGRTVE
LDKKQASYLSYAYATTVHKSQRA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
Auxiliary protein
| ID | 1033 | GenBank | WP_001749975 |
| Name | WP_001749975_p4-IPM |
UniProt ID | A0A5C2CVS6 |
| Length | 138 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 138 a.a. Molecular weight: 15332.60 Da Isoelectric Point: 5.9670
>WP_001749975.1 MULTISPECIES: hypothetical protein [Gammaproteobacteria]
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER
MPIITAKVSDELLAYIDLVSGGNRSDYLRRCIEAGPGDRESGLKIVADRLSDVNRKLDYLFDRASDADFG
PLRDELKAITETLSGVKFPPAGQMMLHESLAIETLILLRSIAEPGKTKAAKAEVERNGYKVWEPKKER
Protein domains
No domain identified.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A5C2CVS6 |
T4CP
| ID | 2185 | GenBank | WP_000342688 |
| Name | t4cp2_I3B51_RS00260_p4-IPM |
UniProt ID | _ |
| Length | 509 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 509 a.a. Molecular weight: 57762.87 Da Isoelectric Point: 9.6551
>WP_000342688.1 MULTISPECIES: type IV secretion system DNA-binding domain-containing protein [Enterobacterales]
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI
MDDRERGLAFLFAITLPPVMVWFLVAKFTYGIDPSTAKYLIPYLVKNTFSLWPLWSALIAGWFIGVGGLI
AFIIYDKSRVFKGERFKKIYRGTELVRARTLADKTRERGVNQLTVANIPIPTYAENLHFSIAGTTGTGKT
TIFNELLFKSIIRGGKNIALDPNGGFLKNFYRPGDVILNAYDKRTEGWVFFNEIRRSYDYERLVNSIVQE
SPDMATEEWFGYGRLIFSEVSKKLHSLYSTVTMEEVIHWACNVDQKKLKEFLMGTPAEAIFSGSEKAVGS
ARFVLSKNLAPHLKMPEGNFSLRDWLDDGKPGTLFITWQEEMKRSLNPLISCWLDSIFSIVLGMGEKESR
INVFIDELESLQFLPNLNDALTKGRKSGLCVYAGYQTYSQLVKVYGRDMAQTILANMRSNIVLGGSRLGD
ETLDQMSRSLGEIEGEVERKESDPQKPWIVRKRRDVKVVRAVTPTEISMLPNLTGYLALPGDMPVAKFKA
KHVKYHRKNPVPGIELREI
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 21149..31485
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| I3B51_RS00095 | 17622..17894 | + | 273 | Protein_19 | IS1 family transposase | - |
| I3B51_RS00100 | 18218..19198 | - | 981 | WP_000082736 | IS5-like element ISEc68 family transposase | - |
| I3B51_RS00400 | 19239..19667 | - | 429 | WP_227626567 | restriction endonuclease | - |
| I3B51_RS00110 | 19717..19950 | - | 234 | WP_001191790 | hypothetical protein | - |
| I3B51_RS00115 | 20064..20378 | - | 315 | WP_001749965 | TrbM/KikA/MpfK family conjugal transfer protein | - |
| I3B51_RS00120 | 20375..20719 | - | 345 | WP_001749964 | hypothetical protein | - |
| I3B51_RS00125 | 20735..21106 | - | 372 | WP_011867773 | H-NS family nucleoid-associated regulatory protein | - |
| I3B51_RS00405 | 21149..21487 | + | 339 | WP_227626568 | hypothetical protein | virB1 |
| I3B51_RS00135 | 21899..22184 | + | 286 | Protein_27 | transcriptional repressor KorA | - |
| I3B51_RS00140 | 22194..22487 | + | 294 | WP_001749962 | hypothetical protein | virB2 |
| I3B51_RS00145 | 22537..22854 | + | 318 | WP_000496058 | VirB3 family type IV secretion system protein | virB3 |
| I3B51_RS00150 | 22854..25454 | + | 2601 | WP_001749961 | VirB4 family type IV secretion/conjugal transfer ATPase | virb4 |
| I3B51_RS00155 | 25472..26185 | + | 714 | WP_001749960 | type IV secretion system protein | virB5 |
| I3B51_RS00160 | 26193..26420 | + | 228 | WP_001749959 | IncN-type entry exclusion lipoprotein EexN | - |
| I3B51_RS00165 | 26436..27476 | + | 1041 | WP_001749958 | type IV secretion system protein | virB6 |
| I3B51_RS00170 | 27547..27705 | + | 159 | WP_012561180 | hypothetical protein | - |
| I3B51_RS00175 | 27695..28393 | + | 699 | WP_000646594 | type IV secretion system protein | virB8 |
| I3B51_RS00180 | 28404..29288 | + | 885 | WP_000735066 | TrbG/VirB9 family P-type conjugative transfer protein | virB9 |
| I3B51_RS00185 | 29288..30448 | + | 1161 | WP_000101710 | type IV secretion system protein VirB10 | virB10 |
| I3B51_RS00190 | 30490..31485 | + | 996 | WP_000128596 | ATPase, T2SS/T4P/T4SS family | virB11 |
| I3B51_RS00195 | 31485..32018 | + | 534 | WP_000792636 | phospholipase D family protein | - |
| I3B51_RS00415 | 32193..32480 | - | 288 | Protein_40 | DUF6710 family protein | - |
| I3B51_RS00210 | 32748..32927 | + | 180 | Protein_41 | helix-turn-helix domain-containing protein | - |
| I3B51_RS00215 | 32992..33696 | + | 705 | WP_001067855 | IS6-like element IS26 family transposase | - |
| I3B51_RS00220 | 33750..34381 | - | 632 | Protein_43 | transposase | - |
| I3B51_RS00225 | 34776..35433 | + | 658 | Protein_44 | quinolone resistance pentapeptide repeat protein QnrS1 | - |
| I3B51_RS00230 | 35752..36366 | - | 615 | WP_014839983 | recombinase family protein | - |
Host bacterium
| ID | 3683 | GenBank | NZ_KY913900 |
| Plasmid name | p4-IPM | Incompatibility group | IncN |
| Plasmid size | 61680 bp | Coordinate of oriT [Strand] | 44237..44337 [+] |
| Host baterium | Klebsiella oxytoca strain pKOX3 |
Cargo genes
| Drug resistance gene | blaIMP-4, qnrS1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |